Abstract Reactive oxygen species (ROS) are involved in both bone and cartilage physiology and play an important role in the pathogenesis of osteoporosis and osteoarthritis. The present study investigated the effect of running exercise on bone and cartilage in heterozygous manganese superoxide dismutase (SOD2)-deficient mice. It was hypothesized that exercise might induce an increased production of ROS in these tissues. Heterozygous SOD2-deficient mice should exhibit an impaired capability to compensate, resulting in an increased oxidative stress in cartilage and bone. Thirteen female wild type and 20 SOD2(+/?) mice (aged 16 weeks) were randomly assigned to a non-active wild type (SOD2(+/+)Con, n = 7), a trained wild type (SOD2(+/+)Run, n = 6), a non-active SOD2(+/?) (SOD2(+/?)Con, n = 9) and a trained SOD2(+/?) (SOD2(+/?)Run, n = 11) group. Training groups underwent running exercise on a treadmill for 8 weeks. In SOD2(+/?) mice elevated levels of 15-F(2t)-isoprostane and nitrotyrosine were detected in bone and articular cartilage compared to wild type littermates. In osteocytes the elevated levels of these molecules were found to be reduced after exercise while in chondrocytes they were increased by aerobic running exercise. The observed changes in oxidative and nitrosative stress did neither affect morphological, structural nor mechanical properties of both tissues. These results demonstrate that exercise might protect bone against oxidative stress in heterozygous SOD2-deficient mice.